The BARE-1 retrotransposon is a major, active component of the genome of barley (Hordeum vulgareL.) and other Hordeum species. Copia-like in its organization, it consists of 1.8-kb long terminal repeats bounding an internal domain of 5275bp which encodes a predicted polyprotein of 1301 residues. The polyprotein contains the key residues, structural motifs, and conserved regions associated with retroviral and retrotransposon GAG, aspartic proteinase, integrase, reverse transcriptase, and RNaseH polypeptides. BARE-1 is actively transcribed and translated. As part of our effort to understand the evolution and function of BARE-1, we have examined its copy number and localization. Full-length members of the BARE-1 family constitute 2.8% of the barley genome. Globally, they are dispersed throughout the genome, excepting the centromeric, telomeric, and NOR regions. Locally, BARE-1 occurs more commonly in repetitive DNA than in coding regions, forming clusters of nested insertions. Both barley and other Hordeum genomes contain a high proportion of BARE-1 solo LTRs. New techniques have been developed which exploit the insertion site polymorphism generated by -1 integration to produce molecular markers for breeding, biodiversity, and mapping applications.

The work presented here received support under the European Union Directorate for Biotechnology research program on Molecular Tools for Biodiversity as well as under the Genome Research Programme ofthe Academy of Finland.

Peer reviewed